Comparison between the types for the ages (after controlling for gender)

Questions

• What are the differences between the types for the ages?
• Do we observe the same changes as globally?

Loads

Libraries and functions

==========================================================================
*
*  Package WGCNA 1.63 loaded.
*
*    Important note: It appears that your system supports multi-threading,
*    but it is not enabled within WGCNA in R. 
*    To allow multi-threading within WGCNA with all available cores, use 
*
*          allowWGCNAThreads()
*
*    within R. Use disableWGCNAThreads() to disable threading if necessary.
*    Alternatively, set the following environment variable on your system:
*
*          ALLOW_WGCNA_THREADS=<number_of_processors>
*
*    for example 
*
*          ALLOW_WGCNA_THREADS=4
*
*    To set the environment variable in linux bash shell, type 
*
*           export ALLOW_WGCNA_THREADS=4
*
*     before running R. Other operating systems or shells will
*     have a similar command to achieve the same aim.
*
==========================================================================


Allowing multi-threading with up to 4 threads.

preparing gene to GO mapping data...
preparing IC data...
preparing gene to GO mapping data...
preparing IC data...
preparing gene to GO mapping data...
preparing IC data...

Data

Stats

	Wald padj < 0.05	LFC > 0 (Wald padj < 0.05)	LFC < 0 (Wald padj < 0.05)
GF VS SPF (8w)	1.63	0.87	0.76
GF VS SPF (52w)	3.76	1.50	2.26
GF VS SPF (104w)	12.66	5.42	7.24

Differentially expressed genes

Warning message in grep(txdbPattern, installedPackages):
“argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G):
“initial point very close to some inequality constraints”Warning message in grep(txdbPattern, installedPackages):
“argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G):
“initial point very close to some inequality constraints”Warning message in grep(txdbPattern, installedPackages):
“argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G):
“initial point very close to some inequality constraints”Warning message in grep(txdbPattern, installedPackages):
“argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G):
“initial point very close to some inequality constraints”

Counts

GF != SPF for 8w with abs(FC) > 2

GF != SPF for 52w with abs(FC) > 2

GF != SPF for 104w with abs(FC) > 2

Comparison of the numbers per ages

Differentially expressed genes

DEG into gene co-expression network

• White: up-regulated
• Black: down-regulated

8w

52w

104w

Global

GO analysis

Biological process

Dot-plot with the most over-represented BP GO (20 most significant p-values for the different comparison)

Network based on description similarity

8w

52w

104w

Global

Cellular components

Dot-plot with the most over-represented CC GO (20 most significant p-values for the different comparison)

Warning message:
“Removed 4 rows containing missing values (geom_point).”

Molecular functions

Dot-plot with the most over-represented MF GO (20 most significant p-values for the different comparison)

Warning message:
“Removed 4 rows containing missing values (geom_point).”

KEGG pathways

[1] "Note: 9 of 3810 unique input IDs unmapped."
[1] "Note: 9 of 3810 unique input IDs unmapped."
[1] "Note: 9 of 3810 unique input IDs unmapped."
[1] "Note: 9 of 3810 unique input IDs unmapped."

Pathway graphs available at ../results/dge/type-effect/type_gender/over_repr_kegg/

[1] "Note: 9 of 3810 unique input IDs unmapped."

Warning message in file.rename(from = paste("mmu", cat, ".pathview.multi.png", sep = ""), :
“cannot rename file 'mmu00511.pathview.multi.png' to '../results/dge/type-effect/type_age/under_repr_kegg/mmu00511.pathview.multi.png', reason 'No such file or directory'”

Pathway graphs available at ../results/dge/type-effect/type_gender/under_repr_kegg/